specifying chromosome does not map aliases if gene is correct on another chromosome

Question

specifying chromosome does not map aliases if gene is correct on another chromosome

Opened this issue 4 years ago · 7 comments

Here is an example. @Aggarwal-Ayush would you see if you can fix this?

library(HGNChelper)
#> Please cite our software :) 
#>  
#>  Sehyun Oh et al. HGNChelper: identification and correction of invalid gene symbols for human and mouse. F1000Research 2020, 9:1493. DOI: https://doi.org/10.12688/f1000research.28033.1 
#>  
#>  Type `citation('HGNChelper')` for a BibTeX entry.
hgnc.table[hgnc.table$Symbol == "TKT" | hgnc.table$Approved.Symbol == "TKT", ]
#>    Symbol Approved.Symbol chromosome
#> 1:    TKT            DDR2          1
#> 2:    TKT             TKT          3
checkGeneSymbols(c("TKT", "TKT"), chromosome = c(1, 3))
#> Maps last updated on: Mon Sep 28 18:31:21 2020
#>     x Approved Suggested.Symbol Input.chromosome Correct.chromosome
#> 1 TKT     TRUE              TKT                1                  1
#> 2 TKT     TRUE              TKT                3                  3

The desired behavior for a unit test would be:

library(testthat)
library(HGNChelper)
res <- checkGeneSymbols(c("TKT", "TKT"), chromosome = c(1L, 3L))
expect_identical(res$Approved, c(FALSE, TRUE))
expect_identical(res$Suggested.Symbol, c("DDR2", "TKT"))
expect_identical(res$Input.chromosome, c(1L, 3L))
expect_identical(res$Correct.chromosome, c(1L, 3L))

Answer 1 · 2021-01-13T06:00:29.000Z

Sure. I'll fix it.

Answer 2 · 2021-01-28T09:25:58.000Z

@Aggarwal-Ayush just checking if this is still on your radar?

Answer 3 · 2021-01-28T09:34:54.000Z

@lwaldron This issue was resolved in my last PR.

Answer 4 · 2021-01-28T10:07:51.000Z

I mean the error it introduced in R CMD CHECK... -- Levi Waldron Associate Professor Department of Epidemiology and Biostatistics CUNY Graduate School of Public Health and Health Policy Institute for Implementation Science in Population Health 55 W 125th St, New York NY 10035 https://waldronlab.io

Answer 5 · 2021-01-28T10:48:54.000Z

Yes, that I'm looking into but so far I've not been able to find the cause of that error. I'll check again.

Answer 6 · 2021-03-25T08:40:55.000Z

Hi @Aggarwal-Ayush I just did some other minor updates and am getting ready to update CRAN in advance of posting the response to reviewers. Any luck?

Answer 7 · 2021-03-25T10:40:58.000Z

Hi @lwaldron All the checks were passed in my last PR. This issue can be closed now.